FFPE stands for Formalin-Fixed Paraffin-Embedded. FFPE samples are a valuable way of preserving biomaterial for long-term research. Biomaterials preserved in this way can be used also for retrospective studies.

DNA extraction from FFPE paraffin media / paraffin blocks is used in molecular diagnostics and oncology research.

However, isolation of DNA from FFPE samples is challenging because formalin used for tissue fixation can damage DNA, leading to DNA fragmentation and degradation. In addition, paraffin wax used to embed tissues in blocks can also make DNA isolation difficult.

To isolate DNA from FFPE, we recommend using the D-FFPE kit. The kit contains all the necessary reagents and instructions to perform the process. The principle of the kit is based on selective sorption of nucleic acids from a pre-lysed sample on a silica membrane, subsequent washing and elution of the purified product.

DNA isolated by D-FFPE kit can be used for various molecular biological studies: PCR, PCR-RV, nick-translation, sequencing, genotyping, SNP analysis and others.

First, you should prepare samples for work - make slices up to 10 µm thick.

Next, dewax the samples - place the slices in dewaxing buffer, incubate, mix and centrifuge, then remove the supernatant without capturing tissue sediment. The D-FFPE kit includes a dewaxing buffer that is free of toxic and volatile components (odorless).

When the sample is paraffinized, it should be lysed according to the D-FFPE kit protocol, and RNA impurities removed if RNA purification is required. The kit contains RNase A to purify the isolated sample from RNA impurities.

The sample is then applied to the column and centrifuged, after which the column is washed.

To obtain the eluate, the column should be transferred to a new microtube, and pre-warmed elution buffer should be applied to the center of the column filter, incubated and then centrifuged. The resulting eluate should be stored at -20°C.

The amount of DNA to be extracted is up to 10 µg.

The integrity of the isolated DNA can be verified by performing PCR on long fragments (500 bp or more). After PCR, amplification products should be checked by gel electrophoresis in 1% agarose gel.

The kit allows for gentle DNA extraction and obtaining DNA fragments longer than 1000 bp by removing PCR inhibitors.